Contacts of the helix formed by residues 357 - 372 (chain J) in PDB entry 2ABJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 357 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J PHE* 3.7 25.1 - - + -
325J GLU* 3.4 16.4 - - - +
337J PRO* 4.6 0.9 - - + -
352J THR* 3.5 22.9 - - + +
353J MET* 3.8 30.3 - - + -
355J ASN 3.5 2.2 - - - +
356J GLY* 1.3 81.6 - - - +
358J LYS* 1.3 59.3 + - - +
359J LEU 3.5 1.3 - - - -
360J ALA* 3.7 11.2 - - + -
361J SER* 2.6 42.1 + - - +
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Residues in contact with LYS 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J TYR* 4.9 6.0 + - + +
272J GLU* 5.8 0.2 + - - -
324J ARG* 3.5 30.8 - - - +
325J GLU* 3.3 5.9 + - - +
355J ASN 2.9 18.5 + - - +
356J GLY* 3.4 4.3 - - - -
357J PRO* 1.3 71.1 - - - +
359J LEU* 1.3 63.3 + - + +
361J SER* 3.9 2.9 - - - -
362J ARG* 3.1 28.1 + - + +
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Residues in contact with LEU 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J TYR* 3.7 31.4 - - + -
274J LEU* 3.7 32.1 - - + -
299J TRP* 3.8 28.9 - - + -
302J PHE* 3.8 21.8 - - + -
325J GLU* 2.8 20.9 + - - +
327J PHE* 4.4 3.1 - - + -
358J LYS* 1.3 75.4 - - + +
360J ALA* 1.3 59.8 + - - +
362J ARG* 3.0 13.6 + - - +
363J ILE* 2.8 43.5 + - + +
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Residues in contact with ALA 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J PHE* 4.0 4.9 - - + -
325J GLU* 2.8 19.9 + - - +
327J PHE* 4.2 19.6 - - + -
335J VAL* 3.8 28.3 - - + +
337J PRO* 5.2 4.0 - - + -
352J THR* 5.4 0.9 - - + -
357J PRO* 3.7 18.4 - - + -
359J LEU* 1.3 73.4 - - - +
361J SER* 1.3 56.7 + - - +
363J ILE* 3.5 3.6 + - - +
364J LEU* 3.0 29.5 + - - +
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Residues in contact with SER 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J PHE* 3.8 19.6 - - - -
356J GLY 4.8 0.7 - - - -
357J PRO* 2.6 31.7 + - - +
358J LYS* 3.9 3.6 - - - -
360J ALA* 1.3 73.8 - - - +
362J ARG* 1.3 59.7 + - - +
364J LEU* 3.4 3.2 + - - +
365J SER* 3.0 36.8 + - - -
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Residues in contact with ARG 362 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J TRP* 3.5 58.8 - - + +
301J GLU* 2.8 43.2 + - - -
302J PHE* 4.9 5.9 - - - -
358J LYS* 3.1 17.5 + - - +
359J LEU* 3.0 15.9 + - + +
361J SER* 1.3 77.9 - - - +
363J ILE* 1.3 56.4 + - - +
365J SER* 3.7 5.4 - - - -
366J LYS* 3.0 28.7 + - + +
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Residues in contact with ILE 363 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J LEU* 5.2 1.1 - - + -
292J ILE* 3.7 30.7 - - + -
295J LEU* 5.2 5.2 - - + -
299J TRP* 4.1 20.4 - - + -
327J PHE* 3.6 33.7 - - + -
335J VAL* 3.9 13.2 - - + -
359J LEU* 2.8 37.0 + - + +
360J ALA* 3.8 3.8 - - - +
362J ARG* 1.3 71.0 - - - +
364J LEU* 1.3 61.5 + - - +
366J LYS* 3.8 4.8 - - - +
367J LEU* 2.8 54.8 + - + +
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Residues in contact with LEU 364 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J PHE* 4.0 29.2 - - + -
197J PHE* 3.4 32.8 - - + -
333J CYS 4.4 5.6 - - - +
334J VAL* 3.7 39.3 - - + -
335J VAL* 4.9 2.6 - - + +
360J ALA 3.0 17.6 + - - +
361J SER* 3.4 4.9 + - - +
363J ILE* 1.3 75.9 - - - +
365J SER* 1.3 57.9 + - - +
367J LEU* 3.9 0.5 - - - +
368J THR* 2.8 49.2 + - + +
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Residues in contact with SER 365 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J SER* 3.0 20.0 + - - -
362J ARG* 3.7 6.5 - - - -
364J LEU* 1.3 78.7 - - - +
366J LYS* 1.3 56.8 + - - +
368J THR* 3.2 6.6 + - - -
369J ASP* 2.9 39.6 + - - +
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Residues in contact with LYS 366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295J LEU* 4.0 28.0 - - + -
299J TRP* 4.2 26.8 - - + +
362J ARG* 3.0 19.5 + - + +
363J ILE* 3.8 5.8 - - - +
365J SER* 1.3 75.1 - - - +
367J LEU* 1.3 64.3 + - - +
369J ASP* 3.4 12.1 + - - +
370J ILE* 3.2 35.4 + - + +
375J GLU* 3.2 27.2 + - - +
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Residues in contact with LEU 367 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J PHE* 4.2 13.2 - - + -
288J THR* 3.9 21.5 - - + +
291J CYS* 4.0 10.3 - - + -
292J ILE* 4.1 6.7 - - + -
295J LEU* 3.8 23.8 - - + -
334J VAL* 3.7 23.1 - - + -
363J ILE* 2.8 40.8 + - + +
364J LEU 4.1 2.0 - - - +
366J LYS* 1.3 74.7 - - - +
368J THR* 1.3 55.4 + - - +
370J ILE* 3.4 6.5 + - + +
371J GLN* 2.9 41.7 + - - +
379J TRP* 4.0 19.3 - - + -
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Residues in contact with THR 368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J THR 5.6 1.6 - - - +
192J PHE* 5.9 3.6 - - + -
334J VAL* 4.6 5.6 - - + -
364J LEU* 2.8 47.7 + - + +
365J SER* 3.2 9.2 + - - -
367J LEU* 1.3 72.4 - - - +
369J ASP* 1.3 70.1 + - - +
371J GLN* 3.7 17.5 - - - +
372J TYR* 2.9 46.9 + - + +
374J ARG* 5.8 0.7 - - - -
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Residues in contact with ASP 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J SER* 2.9 28.4 + - - +
366J LYS* 3.5 14.1 - - - +
368J THR* 1.3 77.5 + - - +
370J ILE* 1.3 61.8 + - - +
372J TYR 3.8 0.2 - - - -
373J GLY 3.2 2.9 + - - -
374J ARG* 2.7 65.9 + - + +
375J GLU* 3.2 15.2 + - + +
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Residues in contact with ILE 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J PHE* 3.8 19.5 - - + -
295J LEU* 4.9 3.8 - - + -
366J LYS* 3.2 29.7 + - + +
367J LEU* 3.6 9.6 - - + +
369J ASP* 1.3 74.3 - - - +
371J GLN* 1.3 66.2 + - - +
373J GLY* 3.1 13.7 + - - -
375J GLU* 3.7 40.8 - - + +
377J SER* 4.0 22.4 - - - +
379J TRP* 3.9 29.4 - - + -
380J THR* 3.4 21.8 + - + +
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Residues in contact with GLN 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J PHE* 3.3 63.8 - - + +
107J ARG* 4.0 15.4 + - - +
109J PHE* 3.7 32.7 - - + -
331J THR 5.8 1.6 + - - -
334J VAL* 4.6 16.6 - - - +
367J LEU* 2.9 31.0 + - - +
368J THR* 3.3 22.3 + - - +
370J ILE* 1.3 76.4 - - - +
372J TYR* 1.3 61.3 + - + +
373J GLY 3.6 0.5 + - - -
380J THR* 4.2 7.4 - - - +
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Residues in contact with TYR 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J PHE* 3.7 32.0 - + + -
100J ARG 3.3 25.4 - - - -
101J GLY* 3.1 9.8 - - - -
102J VAL* 2.9 34.9 + - + +
107J ARG* 4.2 0.9 - - - -
153J SER 3.6 18.4 - - - -
154J THR* 3.3 30.9 + - + -
155J SER* 3.7 2.6 - - - -
156J ALA 2.8 34.1 + - - -
157J SER* 4.1 1.2 - - - -
368J THR* 2.9 43.9 + - + +
369J ASP 4.6 0.7 - - - +
371J GLN* 1.3 78.2 - - + +
373J GLY* 1.3 61.0 + - - +
374J ARG* 3.3 8.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il